[Gate-users] TPS Pencil Beam Source setting

Mon May 25 09:07:30 CEST 2020

Dear Hui Zhang,
If I understand your issue, you are trying to reproduce the behavior of the PBS source using the TPS source.

In this case, I would suggest to place a phase space right after particle generation of both the PBS and the TPS source and analyze the particle position distribution (mean position and standard deviation), particle angular distribution (mean angle and standard deviation), energy distribution (mean energy and energy spread), in order to verify that both source provide the same output.
Be careful about units: for example the energy spread can be given in absolute MeV or as percentage of the mean energy.

Hope this helps.

Best,
Loïc

From: 张晖 [mailto:zhanghui at impcas.ac.cn]
Sent: Montag, 25. Mai 2020 03:57
To: Grevillot Loic <loic.grevillot at medaustron.at>
Cc: gate-users at lists.opengatecollaboration.org
Subject: Re: RE: [Gate-users] TPS Pencil Beam Source setting

Dear Loïc,

Thanks for your advice! It really helps to enhance my understanding about the TPS Pencil Beam Source from the link you provided. My confusion is that how to set the parameters in Source-Properties.txt file of TPS Pencil Beam Source, if I want to make the dose distributions in water consistent with the results from Pencil Beam Source setting.

In Pencil Beam Source simulation, the source position was located before the vacuum window and a water box was located at isocenter. The energy spread, spot size (x and y), divergence (theta and phi), beam emittance(x-theta,y-phi) were set to 0.1% of the respective energy,3 mm,4 mrad and 15 mm·mrad. All beams are converging.

In TPS Pencil Beam Source simulation, "Nozzle exit to Isocenter distance" was set to the position of the vacuum window.

However, I find that the dose distributions with these two sources in water box were different, such as percentage depth dose (PDD).

Now, I doubt that my parameter settings in TPS Pencil Beam Source simulation might be wrong. How can I do?

#################Pencil Beam Source########################################

# SOURCE PBS
/gate/source/addSource C12 PencilBeam

#particle type
/gate/source/C12/setParticleType GenericIon
/gate/source/C12/setIonProperties 6 12 6 0

#energy spectrum
/gate/source/C12/setEnergy 2687.52 MeV
/gate/source/C12/setSigmaEnergy 2.68752 MeV

#position
/gate/source/C12/setPosition 0 0 -1.4059 m

# spot size
/gate/source/C12/setSigmaX 3 mm
/gate/source/C12/setSigmaY 3 mm

#divergence
/gate/source/C12/setSigmaTheta 4 mrad
/gate/source/C12/setSigmaPhi 4 mrad

#emittance
/gate/source/C12/setEllipseXThetaEmittance 15 mm*mrad
/gate/source/C12/setEllipseYPhiEmittance 15 mm*mrad

#positive-> converging beam; negative diverging beam
/gate/source/C12/setEllipseXThetaRotationNorm positive
/gate/source/C12/setEllipseYPhiRotationNorm positive

#################TPS Pencil Beam Source-Source-properties########################################

# Source properties

# Nozzle exit to Isocenter distance
1365.4
# SMX to Isocenter distance
4000
# SMY to Isocenter distance
4000

# ENERGY
# mean energy
# polynomial order
1
# polynomial parameters (highest to lowest)
1
0

# energy spread
# polynomial order
percent
1
# polynomial parameters (highest to lowest)
0.001
0

# SPOT x y theta phi
# x
# polynomial order
1
# polynomial parameters
0
3
# Theta
# polynomial order
1
# polynomial parameters
0
0.004
# y
# polynomial order
1
# polynomial parameters
0
3
# Phi
# polynomial order
1
# polynomial parameters
0
0.004

# SPOT emmittances
# x-theta emmittance
# polynomial order
1
# polynomial parameters
0
0.015
# y-phi emmittance
# polynomial order
1
# polynomial parameters
0
0.015

Best regards,

Hui Zhang

-----原始邮件-----
发件人:"Grevillot Loic" <loic.grevillot at medaustron.at<mailto:loic.grevillot at medaustron.at>>
发送时间:2020-05-20 15:58:44 (星期三)
收件人: jbaran <jbaran at ifj.edu.pl<mailto:jbaran at ifj.edu.pl>>, "张晖" <zhanghui at impcas.ac.cn<mailto:zhanghui at impcas.ac.cn>>
抄送: "gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>" <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
主题: RE: [Gate-users] TPS Pencil Beam Source setting

Dear both,

I was having a short look at your discussion and I do not exactly get your issue, but I would like to provide a few hints if it may help:

1.       In the TPS source, one can set the following option to true or false, depending if you want the beam to be diverging or converging:

o   /gate/source/PBS/setBeamConvergence true (or false)

[cid:image001.jpg at 01D63273.EA5B05F0]

o   If you use this option, I do not understand why you would need to change the source code or recompile? Just use the setBeamConvergence option.

o   For a more detailed understanding of the TPS source, you can run the validation tests provided in the GATE-RTion folder<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGateContrib%2Ftree%2Fmaster%2FGATE-RTion%2FTPSPencilBeamSource&data=02%7C01%7Cloic.grevillot%40medaustron.at%7C1edaae2a222148f8c00e08d8004edbf6%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637259686014018643&sdata=xLX9CVJctppYj3XdbC5%2FoqHibxbRMB170pSSrj5Sb8w%3D&reserved=0> of the GitContrib repository of GATE

2.       If despite changing this option, the beam is always diverging, it may simply be that you define your beam properties at the waist position… then in that case the beam can only diverge.

o   [/coremail/s?func=mbox:getComposeData&sid=HAfrCzTTWITexzfcKvTTNfJLaFflOAjO&composeId=1590138788883&attachId=2]

Hope this helps?

Best,
Loïc

-----Original Message-----
From: Gate-users [mailto:gate-users-bounces at lists.opengatecollaboration.org] On Behalf Of jbaran
Sent: Dienstag, 19. Mai 2020 12:17
To: 张晖 <zhanghui at impcas.ac.cn<mailto:zhanghui at impcas.ac.cn>>
Cc: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] TPS Pencil Beam Source setting

Dear Hui Zhang,

maybe this is trivial (I am sorry if I write obvious things), but I want to clarify it. Whenever you change the source code of GATE you have to recompile it. Assuming you have GATE ver.8.2, you have to go to the directory gate_v8.2-build

(https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fcompilation_instructions.html%23compilation-instructions-label&data=02%7C01%7Cloic.grevillot%40medaustron.at%7C7689c7e6677d4cbf737908d7fbdde75d%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637254802831509937&sdata=phmMjoqNL9dXmsyN0zzMkFvqzDJjZ8NHMK%2BT2I5J98Y%3D&reserved=0<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fcompilation_instructions.html%23compilation-instructions-label&data=02%7C01%7Cloic.grevillot%40medaustron.at%7C1edaae2a222148f8c00e08d8004edbf6%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637259686014018643&sdata=pPHl7%2F9oeRTwgl3ECehWni9Rl49mXm0sGN%2FwWYxDRJ4%3D&reserved=0>

this is for GATE 9.0 but the procedure is very similar) and run again

commands:

make -jN (N is the number of processor(s) in your PC) make install

you don't have to build it from the scratch and run commands like ccmake and others, just two commands will be enough (I belive only 'make install' would be sufficient but run both just to be sure). Due to the fact you changed just one file the compilation will be very fast not as it was in case of first compilation.

If you did that already, could you please provide example 2D dose distribution images?

Jakub

On 2020-05-19 11:54, 张晖 wrote:

> Dear Jakub,

> The attachment is the percentage depth dose distribution in water box.

> I just changed the default values on true in

> GateSourceTPSPencilBeam.cc file,and run my code again. Did you mean

> reinstall the Gate 8.2?

>

>

> > -----原始邮件-----

> > 发件人: jbaran <jbaran at ifj.edu.pl<mailto:jbaran at ifj.edu.pl>>

> > 发送时间: 2020-05-19 17:29:00 (星期二)

> > 收件人: "张晖" <zhanghui at impcas.ac.cn<mailto:zhanghui at impcas.ac.cn>> > 抄送:

> gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>

> > 主题: Re: [Gate-users] TPS Pencil Beam Source setting > >

> Dear Hui Zhang, > > just to check, did you recompile the GATE

> once again? Could you please > explain if the differences are in

> spatial distribution or the spatial > distribution of the doses is

> consistent and the differences are in the > values?

> >

> > Jakub

> >

> >

> > On 2020-05-19 11:13, 张晖 wrote:

> > >> Dear Jakub

> > >> I used Gate 8.2 for simulation.In

> GateSourceTPSPencilBeam.cc, the beam > >> is divergent by

> default, and I have changed the default values on > >> true.

> However, it dosen't work in my case.

> > >> #=====================================================

> > >> # BEAMS

> > >> #=====================================================

> > >> /gate/source/addSource PBS TPSPencilBeam > >>

> /gate/source/PBS/setParticleType GenericIon > >>

> /gate/source/PBS/setIonProperties 6 12 6 0 > >>

> /gate/source/PBS/setTestFlag false > >>

> /gate/source/PBS/setPlan data/PlanDescriptionToGATE.txt > >>

> #/gate/source/PBS/setNotAllowedFieldID 1 > >>

> #/gate/source/PBS/setNotAllowedFieldID 2 > >>

> /gate/source/PBS/setFlatGenerationFlag false > >>

> /gate/source/PBS/setSpotIntensityAsNbIons true > >>

> /gate/source/PBS/setSortedSpotGenerationFlag false > >>

> /gate/source/PBS/setSigmaEnergyInMeVFlag false > >>

> /gate/source/PBS/setSourceDescriptionFile

> data/Source-Properties.txt

> > >> /gate/source/PBS/setBeamConvergence true > >>

> > >> This is my part of code in main.mac file.

> > >>

> > >>

> > >> > -----原始邮件-----

> > >> > 发件人: jbaran <jakub.baran at ifj.edu.pl<mailto:jakub.baran at ifj.edu.pl>> > >>

> > 发送时间: 2020-05-19 16:34:13 (星期二)

> > >> > 收件人: "张晖" <zhanghui at impcas.ac.cn<mailto:zhanghui at impcas.ac.cn>> > >>

> > 抄送: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>

> > >> > 主题: Re: [Gate-users] TPS Pencil Beam Source setting

> > >> > > >> > Dear Hui Zhang, > >>

> > > >> > I am not sure which version of GATE you are

> using but from my > >> experience > >> > it seems

> that when you are using Pencil Beam source you are able > >>

> to set > >> > if your beam is divergent or convergent and

> you are using > >> convergent > >> > beam from

> what I see in your souce code. In case of TPS source > >> the

> beam > >> > is divergent by default > >> >

> > >>

> (https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit

> hub.com%2FOpenGATE%2FGate%2Fblob%2Fdevelop%2Fsource%2Fphysics%2Fsrc%2F

> GateSourceTPSPencilBeam.cc&data=02%7C01%7Cloic.grevillot%40medaust

> ron.at%7C7689c7e6677d4cbf737908d7fbdde75d%7Cadb749e06dfd4f6fbea8cd9f8e

> 0c9b89%7C0%7C0%7C637254802831519922&sdata=YQQt8kRb6F9Xf%2BYiVkouea

> 6hf%2BUO0ErAb6eZ0%2FWswZM%3D&reserved=0

> > >> > - lines: 60 and 61), for sure in GATE 8.2 and 9.0

> and I pressume > >> for all > >> > of GATE

> versions is the case but you have to check it with your > >>

> version.

> > >> > In my case I just change the default values on true

> (lines: 60

> > >> and 61)

> > >> > and recompile GATE once again. Please let us know

> if it works in > >> your > >> > case.

> > >> >

> > >> > All the best,

> > >> > Jakub

> > >> >

> > >> >

> > >> >

> > >> > On 2020-05-19 10:19, 张晖 wrote:

> > >> > > Dear Gate Users:

> > >> > >

> > >> > >  I previously used Pencil Beam Source to

> simulate > >> single-energy pencil > >> > >

> beam for carbon-ion therapy. The features of the pencil beam >

> >> source > >> > > such as spot size, divergence

> and beam emittance were > >> defined as > >> >

> > follows: 3 mm spot size in both x and y directions, 4 mrad >

> >> divergence > >> > > and 15 mm·mrad beam

> emittance. The energy spread was set to > >> 0.1% of >

> >> > > the respective energy. Except for dipole scanning

> > >> magnets,vacuum pipe > >> > > and window,

> main and sub-dose monitors, a multi-strip > >> ionization

> > >> > > chamber (IC) and a mini ridge filter were

> modeled in my MC > >> > > simulations. The source

> position was located before the > >> vacuum window >

> >> > > and a water box was located at isocenter.

> > >> > >

> > >> > >  #################Pencil Beam > >>

> > > Source########################################

> > >> > >

> > >> > >  # SOURCE PBS

> > >> > > /gate/source/addSource C12 PencilBeam >

> >> > > > >> > > #particle type >

> >> > > /gate/source/C12/setParticleType GenericIon >

> >> > > /gate/source/C12/setIonProperties 6 12 6 0 >

> >> > > > >> > > #energy spectrum >

> >> > > /gate/source/C12/setEnergy 2687.52 MeV >

> >> > > /gate/source/C12/setSigmaEnergy 2.68752 MeV >

> >> > > > >> > > #position > >>

> > > /gate/source/C12/setPosition 0 0 -1.4059 m > >>

> > > > >> > > # spot size > >> > >

> /gate/source/C12/setSigmaX 3 mm > >> > >

> /gate/source/C12/setSigmaY 3 mm > >> > > > >>

> > > #divergence > >> > >

> /gate/source/C12/setSigmaTheta 4 mrad > >> > >

> /gate/source/C12/setSigmaPhi 4 mrad > >> > > >

> >> > > #emittance > >> > >

> /gate/source/C12/setEllipseXThetaEmittance 15 mm*mrad > >>

> > > /gate/source/C12/setEllipseYPhiEmittance 15 mm*mrad >

> >> > > > >> > > #positive-> converging

> beam; negative diverging beam > >> > >

> /gate/source/C12/setEllipseXThetaRotationNorm

> positive

> > >> > > /gate/source/C12/setEllipseYPhiRotationNorm

> positive

> > >> > >

> > >> > >  Now, I want to use TPS Pencil Beam Source to

> simulate > >> realistic > >> > > treatment

> plan for carbon ion therapy. In > >> Source-properties.txt

> file, > >> > > it contains 8 polynomial equations, each

> equation being a > >> function of > >> > > the

> energy at the nozzle entrance.

> > >> > >

> > >> > >  #################TPS Pencil Beam >

> >> > > > >>

> Source-Source-properties########################################

> > >> > >

> > >> > >  # Source properties > >> > >

> > >> > > # Nozzle exit to Isocenter distance >

> >> > > 1405.9 > >> > > # SMX to Isocenter

> distance > >> > > 4000 > >> > > # SMY to

> Isocenter distance > >> > > 4000 > >> >

> > > >> > > # ENERGY > >> > > # mean

> energy > >> > > # polynomial order > >> >

> > 1 > >> > > # polynomial parameters (highest to

> lowest) > >> > > 1 > >> > > 0 >

> >> > > > >> > > # energy spread >

> >> > > # polynomial order > >> > > percent

> > >> > > 1 > >> > > # polynomial

> parameters (highest to lowest) > >> > > 0.001 >

> >> > > 0 > >> > > > >> > > #

> SPOT x y theta phi > >> > > # x > >> > >

> # polynomial order > >> > > 1 > >> > > #

> polynomial parameters > >> > > 0 > >> >

> > 3 > >> > > # Theta > >> > > #

> polynomial order > >> > > 1 > >> > > #

> polynomial parameters > >> > > 0 > >> >

> > 0.004 > >> > > # y > >> > > #

> polynomial order > >> > > 1 > >> > > #

> polynomial parameters > >> > > 0 > >> >

> > 3 > >> > > # Phi > >> > > #

> polynomial order > >> > > 1 > >> > > #

> polynomial parameters > >> > > 0 > >> >

> > 0.004 > >> > > > >> > > # SPOT

> emmittances > >> > > # x-theta emmittance > >>

> > > # polynomial order > >> > > 1 > >>

> > > # polynomial parameters > >> > > 0 >

> >> > > 0.015 > >> > > # y-phi emmittance

> > >> > > # polynomial order > >> > > 1

> > >> > > # polynomial parameters > >> >

> > 0 > >> > > 0.015 > >> > > >

> >> > >  #################TPS Pencil Beam > >>

> > > > >>

> Source-PlanDescriptionToGate########################################

> > >> > >

> > >> > >  #TREATMENT-PLAN-DESCRIPTION > >>

> > > #PlanName > >> > > IMPT

> > >> > > #NumberOfFractions            ***    CURRENTLY

> THIS VALUE IS

> > >> NOT USED

> > >> > >   ***

> > >> > > 1

> > >> > > ##FractionID                ***    CURRENTLY

> THIS VALUE IS

> > >> NOT USED

> > >> > > ***

> > >> > > 1

> > >> > > ##NumberOfFields > >> > > 1

> > >> > > ###FieldsID > >> > > 1 >

> >> > >

> > >> > > #TotalMetersetWeightOfAllFields        ***

> CURRENTLY THIS

> > >> VALUE IS

> > >> > > NOT USED    ***

> > >> > > 662421

> > >> > >

> > >> > > #FIELD-DESCRIPTION > >> > >

> ###FieldID > >> > > 1

> > >> > > ###FinalCumulativeMeterSetWeight    ***

> CURRENTLY THIS

> > >> VALUE IS NOT

> > >> > > USED    ***

> > >> > > 336732

> > >> > > ###GantryAngle (in degrees) > >> >

> > 0

> > >> > > ###PatientSupportAngle            ***

> CURRENTLY THIS

> > >> VALUE IS NOT

> > >> > > USED    ***

> > >> > > 0

> > >> > > ###IsocenterPosition            ***

> CURRENTLY THIS VALUE

> > >> IS NOT

> > >> > > USED    ***

> > >> > > 0 0 0

> > >> > > ###NumberOfControlPoints > >> >

> > 1 > >> > > > >> > >

> #SPOTS-DESCRIPTION > >> > > ####ControlPointIndex >

> >> > > 0

> > >> > > ####SpotTunnedID            ***    CURRENTLY

> THIS VALUE IS

> > >> NOT USED

> > >> > > ***

> > >> > > 0

> > >> > > ####CumulativeMetersetWeight        ***

> CURRENTLY THIS

> > >> VALUE IS NOT

> > >> > > USED    ***

> > >> > > 0

> > >> > > ####Energy (MeV) > >> > >

> 2687.52 > >> > > ####NbOfScannedSpots > >>

> > > 1 > >> > > ####X Y Weight (spot position at

> isocenter in mm, with > >> weight in MU > >> >

> > (default) or number of ions "setSpotIntensityAsNbIons true") >

> >> > > 0 0 100 > >> > > > >> >

> >  I simulated the same energy beam in my > >>

> PlanDescriptionToGate.txt file > >> > > and the spot

> position is at isocenter.

> However, I find that

> > >> the dose

> > >> > > distributions with these two sources in water

> box were > >> different. I'm > >> > > puzzled

> about the parameter settings in TPS Pencil Beam > >> Source

> if I > >> > > want to make them consistent with those

> in Pencil Beam > >> Source > >> > > settings.

> How can I do?

> > >> > >

> > >> > >  Best regards, > >> > > >

> >> > >  Hui Zhang > >> > > > >>

> > > ------------------------- > >> > >

> _______________________________________________

> > >> > > Gate-users mailing list > >> >

> > Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>

> > >> > >

> > >>

> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists

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> > >>

> > >>

> > >> ------------------------------ > >> Zhang

> HuiUniversity of Chinese Academy of Sciences > >> Institute

> of Modern Physics > >>

> </zhanghui at impcas.ac.cn<mailto:/zhanghui at impcas.ac.cn>></jakub.baran at ifj.edu.pl<mailto:/jakub.baran at ifj.edu.pl>>

> > >> _______________________________________________

> > >> Gate-users mailing list

> > >> Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>

> > >>

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>

>

> ------------------------------

> Zhang HuiUniversity of Chinese Academy of Sciences Institute of Modern

> Physics </zhanghui at impcas.ac.cn<mailto:/zhanghui at impcas.ac.cn>></jbaran at ifj.edu.pl<mailto:/jbaran at ifj.edu.pl>>

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Zhang Hui
University of Chinese Academy of Sciences
Institute of Modern Physics

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